Quantitative PCR instrument

A quantitative PCR instrument[1] is a machine that amplifies and detects DNA. It combines the functions of a thermal cycler and a fluorimeter, enabling the process of quantitative PCR.

The first quantitative PCR machine was described in 1993,[2] and two commercial models became available in 1996. By 2009, eighteen different models were offered by seven different manufacturers.[3] Prices range from about 4,300 USD[4] to 150,000 USD[5]

Principal performance dimensions of quantitative PCR instruments are thermal control, fluorimetry and sample throughput.

Thermal control

Efficient performance of quantitative PCR requires rapid, precise, thermal control.

30 cycles of PCR have been demonstrated in less than 10 minutes.[6] Rapid cycling provides several benefits, including, reduced time to result, increased system throughput and improved reaction specificity.[7] In practice however, engineering trade-offs between ease of use, temperature uniformity, and speed, mean that reaction times are typically more than 25 minutes.[3]

Thermal non-uniformity during temperature cycling contributes to variability in PCR[8][9][10] and, unfortunately, some thermocyclers do not meet the specifications claimed by manufacturers.[11] Increasing the speed of thermal cycling generally reduces thermal uniformity, and can reduce the precision of quantitative PCR.[12]

The temperature uniformity also has a direct effect on the ability to discriminate different PCR products by performing melting point analysis.[13] In addition to uniformity, the resolution with which instruments are able to control temperature is a factor which affects their performance when performing high resolution melting analyses.[14]

Therefore, speed, precision and uniformity of thermal control are important performance characteristics of quantitative PCR instruments.

Fluorimetry

Quantitative PCR instruments monitor the progress of PCR, and the nature of amplified products, by measuring fluorescence.

The range of different fluorescent labels that can be monitored, the precision with which they can be measured, and the ability to discriminate signals from different labels, are relevant performance characteristics.

By using an instrument with sufficient optical channels and extensive assay optimisation, up to 7 separate targets can be simultaneously quantified in a single PCR reaction.[15] However, even with extensive optimisation, the effective dynamic range of such multiplex assays is often reduced due to interference between the constituent reactions.[16]

The noise in fluorescence measurements affects the precision of qPCR. It is typically a function of excitation source intensity variation, detector noise and mechanical noise. Multi factorial analysis has suggested that the contribution of mechanical noise is the most important factor, and that systems with no moving parts in their optical paths are likely to provide improved quantitative precision.[10]

In addition, when performing high resolution melting analyses, one factor that affects the sensitivity of heteroduplex detection is fluorimetric precision.[14]

Therefore, the number of optical channels and the level of noise in fluorescence measurements are also important performance characteristics of quantitative PCR instruments.

References
  1. Also sometimes called "real-time PCR instrument".
  2. Higuchi, R.; Dollinger, G.; Walsh, P.S.; Griffith, R. (1992), "Simultaneous amplification and detection of specific DNA sequences", Bio/Technology, 10 (4): 413–7, doi:10.1038/nbt0492-413, PMID 1368485, S2CID 1684150
  3. Logan, J.; Edwards, K. (January 2009). "Chapter 2 An Overview of PCR Platforms". In Saunders, N. (ed.). Real-Time PCR: Current Technology and Applications. Caister Academic Press. ISBN 978-1-904455-39-4.
  4. Open qPCR open source Real-Time PCR machine
  5. Ma, H.; Shieh, K.; Chen, G.; Chen, X.; Chuang, M. (2006), "Application of Real-time Polymerase Chain Reaction (RT-PCR)", The Journal of American Science, 2 (3): 1–15
  6. Raghavan, V.; Whitney, S.; Ebmeier, R.; Padhye, N.; Nelson, M. Viljoen; Gogos, G. (2006), "Thermal analysis of the vortex tube based thermocycler for fast DNA amplification: Experimental and two-dimensional numerical results", Review of Scientific Instruments, 77 (9): 094301, Bibcode:2006RScI...77i4301R, doi:10.1063/1.2338283
  7. Wittwer, C.T.; Garling, D.J. (1991), "Rapid cycle DNA amplification: time and temperature optimization", BioTechniques, 10 (1): 76–83, PMID 2003928
  8. Kim, Y.H.; Yang, I.; Bae, Y.S.; Park, S.R. (2008), "Performance evaluation of thermal cyclers for PCR in a rapid cycling condition", BioTechniques, 44 (4): 495–6, doi:10.2144/000112705, PMID 18476814
  9. Schoder, D.; Schmalwieser, A.; Schauberger, G.; Kuhn, M.; Hoorfar, J.; Wagner, M. (2003), "Physical characteristics of six new thermocyclers", Clin. Chem., 49 (6): 960–3, doi:10.1373/49.6.960, PMID 12765996
  10. Lee, D. -S. (2010). "Real-time PCR Machine System Modeling and a Systematic Approach for the Robust Design of a Real-time PCR-on-a-Chip System". Sensors. 10 (1): 697–718. doi:10.3390/s100100697. PMC 3270864. PMID 22315563.
  11. Schoder, D.; Schmalwieser, A.; Schauberger, G.; Hoorfar, J.; Kuhn, M.; Wagner, M. (2005), "Novel approach for assessing performance of PCR cyclers used for diagnostic testing", J Clin Microbiol, 43 (6): 2724–8, doi:10.1128/jcm.43.6.2724-2728.2005, PMC 1151936, PMID 15956389
  12. Hilscher, C.; Vahrson, W.; Dittmer, D.P. (2005), "Faster quantitative real-time PCR protocols may lose sensitivity and show increased variability", Nucleic Acids Res., 33 (21): e182, doi:10.1093/nar/gni181, PMC 1297710, PMID 16314296
  13. Herrmann, M.; Durtschi, J.; Wittwer, C.; Voelkerding, K. (2007). "Expanded instrument comparison of amplicon DNA melting analysis for mutation scanning and genotyping". Clinical Chemistry. 53 (8): 1544–1548. doi:10.1373/clinchem.2007.088120. PMID 17556647.
  14. Gundry, C.; Vandersteen, J.; Reed, G.; Pryor, R.; Chen, J.; Wittwer, C. (2003). "Amplicon melting analysis with labeled primers: a closed-tube method for differentiating homozygotes and heterozygotes". Clinical Chemistry. 49 (3): 396–406. doi:10.1373/49.3.396. PMID 12600951.
  15. Köppel, R.; Zimmerli, F.; Breitenmoser, A. (2009), "Heptaplex real-time PCR for the identification and quantification of DNA from beef, pork, chicken, turkey, horse meat, sheep (mutton) and goat", European Food Research and Technology, 230: 125–33, doi:10.1007/s00217-009-1154-5, S2CID 96340566
  16. Bahrdt, C.; Krech, A.; Wurz, A.; Wulff, D. (2010). "Validation of a newly developed hexaplex real-time PCR assay for screening for presence of GMOs in food, feed and seed". Analytical and Bioanalytical Chemistry. 396 (6): 2103–2112. doi:10.1007/s00216-009-3380-x. PMID 20101506. S2CID 22657985.
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